Table_4_No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods.XLSX

The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex comprising numerous closely related lineages, which vary in their ability to cause illness in humans and animals. The classification of B. cereus s.l. isolates into species-level taxonomic units is essential for facilitating communication between and among microbiologists, clinicians, public health officials, and industry professionals, but is not always straightforward. A recently proposed genomospecies-subspecies-biovar taxonomic framework aims to provide a standardized nomenclature for this species complex but relies heavily on whole-genome sequencing (WGS). It thus is unclear whether popular, low-cost typing methods (e.g., single- and multi-locus sequence typing) remain congruent with the proposed taxonomy. Here, we characterize 2,231 B. cereus s.l. genomes using a combination of in silico (i) average-nucleotide identity (ANI)-based genomospecies assignment, (ii) ANI-based subspecies assignment, (iii) seven-gene multi-locus sequence typing (MLST), (iv) single-locus panC group assignment, (v) rpoB allelic typing, and (vi) virulence factor detection. We show that sequence types (STs) assigned using MLST can be used for genomospecies assignment, and we provide a comprehensive list of ST/genomospecies associations. For panC group assignment, we show that an adjusted, eight-group framework is largely, albeit not perfectly, congruent with the proposed eight-genomospecies taxonomy, as panC alone may not distinguish (i) B. luti from Group II B. mosaicus and (ii) B. paramycoides from Group VI B. mycoides. We additionally provide a list of loci that capture the topology of the whole-genome B. cereus s.l. phylogeny that may be used in future sequence typing efforts. For researchers with access to WGS, MLST, and/or panC data, we showcase how our recently released software, BTyper3 (https://github.com/lmc297/BTyper3), can be used to assign B. cereus s.l. isolates to taxonomic units within this proposed framework with little-to-no user intervention or domain-specific knowledge of B. cereus s.l. taxonomy. We additionally outline a novel method for assigning B. cereus s.l. genomes to pseudo-gene flow units within proposed genomospecies. The results presented here highlight the backward-compatibility and accessibility of the recently proposed genomospecies-subspecies-biovar taxonomic framework and illustrate that WGS is not a necessity for microbiologists who want to use the proposed nomenclature effectively.

芽孢杆菌属，亦称广义芽孢杆菌属（B. cereus sensu lato，简称 s.l.），是一个包含众多密切相关谱系的物种复合体，其在人类和动物中引起疾病的能力各异。将广义芽孢杆菌属的分离株分类为物种水平的分类单元对于促进微生物学家、临床医生、公共卫生官员和行业专业人士之间的沟通至关重要，但这种分类并非总是一目了然。近期提出的一种基因组物种-亚基因组物种-生物型分类框架旨在为这一物种复合体提供一个标准化的命名法，但该框架在很大程度上依赖于全基因组测序（WGS）。因此，尚不清楚流行的低成本分型方法（例如单基因和多基因位点序列分型）是否与所提出的分类学保持一致。在本研究中，我们采用计算机模拟方法（i）基于平均核苷酸一致性（ANI）的基因组物种分配，（ii）基于ANI的亚基因组物种分配，（iii）七个基因的多基因位点序列分型（MLST），（iv）单个基因位点panC组分配，（v）rpoB等位基因分型，（vi）致病因子检测，对2,231个广义芽孢杆菌属基因组进行了表征。我们发现，使用MLST分配的序列类型（STs）可以用于基因组物种分配，并提供了ST/基因组物种关联的详尽列表。对于panC组分配，我们表明，经过调整的八组框架在很大程度上，尽管并非完美，与所提出的八个基因组物种分类学保持一致，因为仅凭panC可能无法区分（i）B. luti与第二组的B. mosaicus以及（ii）B. paramycoides与第六组的B. mycoides。此外，我们还提供了一份可能用于未来序列分型工作的捕获整个基因组芽孢杆菌属s.l.系统发育拓扑结构的位点列表。对于能够访问WGS、MLST和/或panC数据的科研人员，我们展示了我们最近发布的软件BTyper3（https://github.com/lmc297/BTyper3）的使用方法，该软件可用于将广义芽孢杆菌属分离株分配到所提出的框架内的分类单元，而无需或几乎不需要用户干预或对广义芽孢杆菌属分类学的专业知识。我们还概述了一种将广义芽孢杆菌属基因组分配到所提出的基因组物种内的伪基因流单元的新方法。本研究结果突出了近期提出的基因组物种-亚基因组物种-生物型分类框架的向后兼容性和易用性，并表明WGS并非微生物学家有效使用所提出命名法的必要条件。